GenomeView 1.90: multiple alignments and syntenic mapping

The latest version of GenomeView has two main new features: support for multiple alignments and the ability to display syntenic blocks

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In the rest of the announcement you find a description of the new features with some screen shots.

JAnnot 1.3 is available

JAnnot has now support for a few new data types:

  • Wiggle tracks (continuous valued data), with some parsers and an internal representation
  • Multiple alignment data, with some parsers and internal representation
  • Added support for syntenic block representation

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API docs

JAnnot 1.2 released

JAnnot 1.2 is released. This is the first public release of JAnnot. JAnnot is a Java library to handle biological sequence data. It was developed to handle the data in- and output of GenomeView.

JAnnot is under active development to cater the needs of GenomeView. It is provided as stand-alone library as-is for those interested. At the moment there is little documentation, however this is one of the focus points in the near future.

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API docs

GenomeView 1.8 released

This releases features a major redesign of the plugin architectures that uses the JPF framework more properly and can account for dependencies between the different plugins. Together with this release we have also released two completely new plugins and we have updated the two plugins that were already available. The two new plugins are for NCBI Blast and for SpliceMachine (a splice site prediction program).

GenomeView 1.7.7 released

Version 1.7.7 of GenomeView has been made publicly available. In this released we focused on improving the performance on larger data sets. The goal was to load the entire Arabidopsis thaliana genome with all annotation that is available at TAIR. This is over 120 megabases of sequence and over 530,000 features. To keep the GUI responsive we implemented a number of graceful degradation measures to limit the number of features that should be painted on the screen. Also the number of internal updates has been optimized to improve the speed of the GUI.

GenomeView 1.7.6 released

In release 1.7.6 of GenomeView we have fixed some bugs and added some new features. The two main features are the more compact GUI resulting in a workable program at lower resolution. Furthermore, we have added dual-screen support. When you have more than one screen attached to your computer, GenomeView will detect this and split the GUI over the two screens. We have added some more configuration options and we have tweaked the GUI in some places.

To fix a bug in the physical property module, we have upgraded to ajt-1.22.

GenomeView 1.7.5 released

In this release we have added support for the GENBANK format, we have fixed some bugs and we have upgraded to AJT version1.21.

  • Support for the genbank file format
  • Fixed a bug where the parent of features loaded from a GFF files were not set properly
  • Fixed a bug where loading multiple feature files sometimes crashed the application
  • Upgraded to AJT-1.21
  • Fixed bug were the ChromosomeView could not be saved to PNG or JPG

GenomeView 1.7.4 released

We have further improved the internals of GenomeView and we have implemented a number of new features in the GUI.

  • CDS panel identifies exons with in-frame stop and missing splice sites graphically
  • Any keyword in the description of a feature can be queried at Ensembl and NCBI
  • CDSView now has viewport to show which part is visible in the StructureView
  • Features are now properly wrapped in the EMBL parser
  • GenomeView now remembers the last visited directory
  • Some improvements to the ChromosomeView

GenomeView 1.7.3 released

GenomeView 1.7.3 fixes a number of bugs to improve to user experience. We also improved to logging mechanism to make it easier to diagnose bugs in the future.

  • Progress bars are shown for all data sources
  • Improved the CDS view
  • Improved logging
  • Sponsor logo is by default turned off
  • Show reply of server when saving to URL
  • About dialog contains information where log and configuration files are stored

GenomeView 1.7.2 released

GenomeView 1.7.2 has been released.

The main new feature is an extra panel that displays the structure of the last selected CDS. This is useful when editing a gene structure and you want to check what happens with the exons that are outside of your zoom. Besides this new panel we have added additional configuration options including the possibility to configure the colors of the different types of data.

Besides this new feature we have fixed a number of bugs and did a number of improvements that should make the GUI more user friendly.

  • Changing a strand is now properly registered in the undo-redo stack
  • Display of some undo-redo items is now more human readable
  • CDS overview list now completely behaves properly
  • EMBL parser now correctly save description lines
  • Undo and redo of structural changes will properly update the phase of an exon
  • A progress box is displayed for all loading and saving events
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